Step-by-Step Guide to Installing GROMACS on Windows 10 and 11 — Transcript

Full transcript

1. 0:00[Music]
2. 0:11in this video I'm going to show you how
3. 0:13you can install and run gr Max and vmd
4. 0:17on a Windows machine but before we begin
5. 0:20I should mention that growmax works
6. 0:23better on a Linux machine especially if
7. 0:25your system has a Koda enabled graphic
8. 0:27Cod the gromax perform on a Linux
9. 0:31machine is significantly higher so first
10. 0:33I recommend migrating to Linux for using
11. 0:36growmax as well as other computational
12. 0:39software and you can also have both
13. 0:41Linux and windows on your PC
14. 0:44simultaneously by dividing the partition
15. 0:48of your system storage but if you only
16. 0:50have a laptop or a desktop and just want
17. 0:54to install growmax to practice and learn
18. 0:56the software this video is for you I
19. 0:59always recommend Linux for using
20. 1:01computational software but if you don't
21. 1:03have a Cod enabled graphic Cod and you
22. 1:06only have a Windows system don't bother
23. 1:09Yourself by installing a real Linux on a
24. 1:14real partition of your system because in
25. 1:17this case the performance difference is
26. 1:19not that much and you can install a
27. 1:21Linux inside your Windows system and
28. 1:24then install gromax on it as I'm going
29. 1:26to teach you in this video so what I'm
30. 1:28going to do today is is first installing
31. 1:31a Linux inside windows that is called
32. 1:35WSL windows subsystem for Linux which is
33. 1:39some sort of virtualization and then
34. 1:41install gromax on it using Linux package
35. 1:44manager this is the easiest way to
36. 1:46install gromax and then I'll teach you
37. 1:49how you can compile gromax on
38. 1:52WSL this is a bit harder but in this way
39. 1:56you can have every version of growmax
40. 1:59including the latest one and then I'll
41. 2:01show you how you can download and
42. 2:03install vmd a graphical program for
43. 2:06gromax and finally I'll show you how you
44. 2:09can use these two program on a Windows
45. 2:12system all right let's get started with
46. 2:15installing W usn on Windows and by the
47. 2:18way this is Windows 11 but you can do
48. 2:21the same job on Windows 10 but don't
49. 2:24forget to update Windows before
50. 2:26installing WSL because this feature
51. 2:29don't works on some old non-updated
52. 2:32windows okay first we need to enable the
53. 2:35windows subsystem for Linux I'm going to
54. 2:38press the start button and type control
55. 2:42panel and open it and then I'm going to
56. 2:45click on programs and turn Windows
57. 2:48features on or off then here I'm going
58. 2:52to turn
59. 2:56on virtual machine platform and
60. 3:00Windows Powers shell
61. 3:04and windows subsystem for
62. 3:07Linux so we need to enable the three
63. 3:10features uh actually Windows Powers
64. 3:14shell is not necessary but it's better
65. 3:16to turn it on and I'm going to click on
66. 3:24okay okay to make it work we need to
67. 3:27restart the system and I will be right
68. 3:30back after restarting the
69. 3:36system okay I've restarted the system
70. 3:39and now we can install a Linux
71. 3:41Distribution on
72. 3:43WSL and to do so uh we need to click on
73. 3:48Microsoft store and here in the search
74. 3:52box I'm going to type Ubuntu and if you
75. 3:56don't know what's Ubuntu Ubuntu is a
76. 3:58Linux distribution which means a variant
77. 4:01of Linux and here we have different
78. 4:04version of it and I'm going to go for
79. 4:06the latest LTS version which is 24.0 4
80. 4:10so let's get it and it automatically
81. 4:14install Ubuntu on Windows subsystem for
82. 4:21Linux all right now we can open it from
83. 4:24here or from the start menu but before
84. 4:29open opening Ubuntu I'm going to open
85. 4:31Windows Powershell or Windows
86. 4:34CMD and type WSL exit update and that's
87. 4:40because sometimes WSL won't work without
88. 4:43updating I'm going to press
89. 4:47enter all right it doesn't need an
90. 4:50update because I already installed WSL
91. 4:53update but make sure to update before
92. 4:57opening WSL
93. 5:00and now press start again and I'm going
94. 5:04to click on
95. 5:08Ubuntu okay now please pay attention to
96. 5:10this it says we need to enable
97. 5:13virtualization in the system bios and
98. 5:16actually I disabled virtualization of my
99. 5:19system intentionally to show you this
100. 5:21error because you certainly will get
101. 5:24this error if the virtualization of your
102. 5:26system is not enabled by default I'm not
103. 5:29show you how I enable virtualization on
104. 5:32my system because that def on different
105. 5:36motherboard brand and different
106. 5:39motherboard models and also different
107. 5:41CPUs but that's not a complicated job
108. 5:44and overall procedure is like that you
109. 5:48must restarting your system and then
110. 5:51when rebooting the system press the
111. 5:54delete key to enter the bias settings
112. 5:57and in the bias settings you must find
113. 6:00CPU virtualization and enable it you can
114. 6:03also Google how to enable
115. 6:05virtualization including your
116. 6:08motherboard and CPU brand okay I'm going
117. 6:11to enable virtualization on my system
118. 6:14and I will be right
119. 6:21back all right I've reseted the system
120. 6:24and now I can open Ubuntu from thek
121. 6:27start menu
122. 6:32and it takes a few
123. 6:35minutes okay now I must give it a new
124. 6:38username I'm going to type hose that's
125. 6:41my
126. 6:45name and a new
127. 6:50password and retype
128. 6:56it all right now I have a brand new
129. 6:58buntu Linux inside my windows let me
130. 7:01increase the font size so you can see
131. 7:04everything
132. 7:06better now let's install gmax on it and
133. 7:10the easiest way to install gmax on
134. 7:12Ubuntu is to use its package manager and
135. 7:15a package manager is a program that
136. 7:17automatically download and install
137. 7:20software from online repositories and
138. 7:23make installation quite straightforward
139. 7:26the open to package manager is apt AP
140. 7:29and and it needs administer privilege so
141. 7:33I'm going to put sudu before it and
142. 7:35first thing first we need to update so
143. 7:38I'm going to type update and press
144. 7:41enter and type my
145. 7:52password now the package manager
146. 7:54database is updated so let's search for
147. 8:01chromax app sech
148. 8:05and
149. 8:07chromax as you can see there are few
150. 8:10packages related to chromax but we only
151. 8:12need this
152. 8:14one
153. 8:18so so to up
154. 8:21install
155. 8:25chromax I'm going to type capital y and
156. 8:29press
157. 8:42enter and that's done and to make sure
158. 8:46that the programs installed on the
159. 8:48system I'm going to type GM and press
160. 8:52enter and it shows that the gromax 20
161. 8:5523.3 is installed on the system I'm
162. 8:58going to show you how you can use the
163. 9:00program later on but for now I want to
164. 9:02teach you a more elaborate way of
165. 9:05installing gromax which is installing
166. 9:08using compiling the source code and the
167. 9:11point of it is that you can compile
168. 9:13every version of gromax you can compile
169. 9:16the latest version of gromax and you can
170. 9:19also active a special features of gromax
171. 9:22and to compile gromax first we need it
172. 9:25Source Cod and gromax is a free and open
173. 9:28source software so we can download it
174. 9:30from its website I'll put the link in
175. 9:33the descriptions
176. 9:36and in this page you can find every
177. 9:39version of gromax even very old
178. 9:42ones um I'm going to go for the latest
179. 9:46stable version which is
180. 9:4924.4 and click download in this page um
181. 9:53you can find a link to the source code
182. 9:57okay let's copy the
183. 10:01link
184. 10:03and in the open to in the WSL I'm going
185. 10:08to type w
186. 10:12get and then right
187. 10:16click
188. 10:21okay and this command W get download um
189. 10:27the link of the file
190. 10:31okay now I have a compressed file of the
191. 10:36source code of the G of the gomac source
192. 10:39code and to uncompress the file I
193. 10:41command top XV ZF and then the name of
194. 10:47the
195. 10:51file all right now we have a
196. 10:54uncompressed folder here and this folder
197. 10:58contains the grx source code let me show
198. 11:02you what's inside the folder with ls
199. 11:04command and you can see what's inside it
200. 11:07and now what I'm going to do is first
201. 11:09create a new folder inside the gromax
202. 11:12folder I'll do it using
203. 11:15M directory
204. 11:17command and let's name it
205. 11:21build and then I'm going to go inside
206. 11:25the build folder using CD command now I
207. 11:30can compile the source code inside the
208. 11:32build folder using the C command but
209. 11:36before doing that I have to install a
210. 11:38compiler and some other tools which are
211. 11:41necessary to compile the code but don't
212. 11:44worry we can easily do the installation
213. 11:46using the app
214. 11:49command and to make it even easier I've
215. 11:52put the installation command in Dy
216. 11:54website so you can copy it from
217. 12:00from
218. 12:03here
219. 12:05and just paste it in the command
220. 12:23line okay that's done and now we can
221. 12:25compile the gomac source code using
222. 12:29three simple commands the first one is
223. 12:32the C command you can copy it from
224. 12:39here and just pay attention to this
225. 12:42option this option specified the path of
226. 12:45the chromax binary of the
227. 12:48compilation and this is in the opt
228. 12:51folder and it will create a new folder
229. 12:55name gromax uh-2 24.4 for in the opt
230. 13:01folder this is a arbitrary name you can
231. 13:03name it anything you want but if you
232. 13:06want to install a different version of
233. 13:08gromax name it correctly okay I'm going
234. 13:11to press
235. 13:23enter and now the configuration is
236. 13:27done and I can compile the code using
237. 13:30the make Command and I'm going to use SE
238. 13:34CPU calls and press
239. 13:43end all right it takes a while to do the
240. 13:52[Music]
241. 13:53job all right now the compilation is
242. 13:56done and it has created some binary file
243. 13:59FES so I can install them using sudu
244. 14:03make install
245. 14:05command and press
246. 14:10enter okay the installation's done let's
247. 14:13check the installed program files they
248. 14:16must be in the
249. 14:19opt gromax
250. 14:2224.4 and being fold all right now
251. 14:26because we want to provoke you want to
252. 14:28recall grx command in every location in
253. 14:31every folder we need to Source this file
254. 14:36GMX r. bash in
255. 14:39the um bash RC file of the bash shell
256. 14:45and you can do this easily using this
257. 14:52command but again notice the name of the
258. 14:55gmax folder in the command if you have
259. 14:57changed it in the the previous step you
260. 15:00must change it here to the names must be
261. 15:03exactly the same and then press enter
262. 15:06all right after sourcing the file we
263. 15:08need to restart the B
264. 15:10shell exit and open it
265. 15:20again now if I run GMX command you can
266. 15:24see that the chromax 2024 has installed
267. 15:28on my system also I can check the
268. 15:31location of the program using where is
269. 15:34command where is GMX and it shows that I
270. 15:38have two gromax binary file on my system
271. 15:41one is in the
272. 15:43USR bin folder and the other in the op
273. 15:48folder that's because I have installed
274. 15:50grx in two ways the first one is the one
275. 15:53I have installed using the APT command
276. 15:55and the second one is the compiled one
277. 15:58and actually actually now we don't need
278. 16:00the first one so let's remove it
279. 16:03using apt command so do
280. 16:08app remove
281. 16:13chromax and
282. 16:15yes let's check again and now we only
283. 16:20have one grx binary file which is the
284. 16:23compiled one all right some of you may
285. 16:25ask can I compile chromax with GPU
286. 16:29support in
287. 16:30WSL yes but you shouldn't for creating a
288. 16:34GPU enabled gromax all you need to do is
289. 16:37first installing Koda toolkit and then
290. 16:42compiling grx using GPU equals Cod
291. 16:46option if you are interested I have
292. 16:47another video which shows how you can
293. 16:49compile with GPU support in Linux but I
294. 16:53don't recommend compiling for GPU here
295. 16:56in WL because the performance this isn't
296. 16:59great actually it's awkward and
297. 17:02simulations takes longer time using GPU
298. 17:05than without GPU in WSL okay now let me
299. 17:09show you how you can use gromax and vmd
300. 17:12a graphical program to visualize
301. 17:15molecules in WL in Windows subsystem for
302. 17:19Linux and actually you can't install vmd
303. 17:22here in WSL because it's not a graphical
304. 17:25interface but you don't need to because
305. 17:28you can inst vmd on Windows itself all
306. 17:31you need to do is download the installer
307. 17:35from its website I'll put the link in
308. 17:38the descriptions here I recommend
309. 17:40downloading the latest stable version
310. 17:43and it has two version for Windows one
311. 17:47um openg plus Cod version and one only
312. 17:51opengl version if you have a Nvidia
313. 17:53graphic card download this one the Cod
314. 17:56version and if you don't have download
315. 17:59the openg G version okay you can
316. 18:02download it from here and you have to
317. 18:04register in the website and then it
318. 18:07allows you to download the program and I
319. 18:10already downloaded the program the
320. 18:13install of the program and you can
321. 18:15install it like any usual windows
322. 18:25program okay and then you can open it
323. 18:27from the start men
324. 18:33menu so the installation is quite easy
325. 18:37but a confusing thing is that how you
326. 18:40can access the WSL files in Windows so
327. 18:45that you can use vmd or other programs
328. 18:48you can't access WSL files in Windows
329. 18:52but you can access Windows files and
330. 18:56folders in WSL
331. 19:01to access Windows File system we have to
332. 19:03go
333. 19:04to/ MNT and then here you can find
334. 19:10Windows drivers in this system I have
335. 19:13two partitions c and d and here I can
336. 19:16access contents of each of them using CD
337. 19:20command cd/ mn/ C for
338. 19:24example and here I can see contents of
339. 19:28the C driver let's make a new folder in
340. 19:32the C
341. 19:36driver let's name it
342. 19:39WSL and I'm going to put um sample input
343. 19:45file a sample gromax input file in
344. 19:50there you can download this file from
345. 19:54the website from the silico website I'm
346. 19:58going to put the link in the description
347. 20:00box just download the file from
348. 20:06here and now if I go into the WSL
349. 20:12file I can see the file here I have
350. 20:17created this file this sample simulation
351. 20:19input so that you can test programs
352. 20:23gromax and vmd and find out if they
353. 20:26works properly so this is not for
354. 20:29learning simulation and please don't use
355. 20:32the sample files for real simulations
356. 20:34we'll talk about chromax input files
357. 20:37later on in this workshop and I'll teach
358. 20:39you how you can create but for now this
359. 20:42is just a sample file actually this is a
360. 20:44folder compressed as a file so first
361. 20:47let's extract it using top x with f the
362. 20:52name of the
363. 20:53file all right now we have a folder
364. 20:59here so let's go into
365. 21:05it okay to run a simulation using gromax
366. 21:08first we need to create a binary input
367. 21:12file a gromax binary input file which
368. 21:15has tpr extension using these files uh
369. 21:20actually some of these files and the
370. 21:23command is grp you can find the complete
371. 21:29Command here from the
372. 21:32website I'm going to copy it and paste
373. 21:36it
374. 21:38here all
375. 21:44right we have the simulation input file
376. 21:47here and now we can run the real
377. 21:49simulation using GMX
378. 21:53mdon V and fnm
379. 21:59nvt okay I'm going to press
380. 22:07enter and the simulation's done it was a
381. 22:10very short simulation it only took 11
382. 22:12seconds to complete and as you can see
383. 22:14it used one MPI thread which means it
384. 22:17was on one system one PC and six open MP
385. 22:22thread which means it use six CPU
386. 22:25Calles uh which is good because my syst
387. 22:28system has six CPU Calles and it use all
388. 22:31of the CPU power now if I check output
389. 22:35files I can see that there are new files
390. 22:38in the folder the output of simulation
391. 22:41and this one is a geometry file which
392. 22:44contains geometry of molecules and atoms
393. 22:47and we can open it and see the atomic
394. 22:50system using the vmd
395. 22:54program okay um let me open the vmd
396. 23:11again I'm going to go to the file new
397. 23:15molecule
398. 23:17and the file is in
399. 23:20the C drive and
400. 23:25WL and uh chxr test
401. 23:30folder and um nvt do grow file that's
402. 23:37the geometry file and
403. 23:39open and then
404. 23:42load and here we have the atomic
405. 23:49system all right I'll teach you how you
406. 23:51can use vmd later on but for now that's
407. 23:54how you can access and visualize
408. 23:57simulation results using vmd in Windows